I doubt anyone is interested in helping diagnose a bug in a multithreaded application, but I was hoping someone instead might be able to provide some additional insight into a pytables error message.
I have a multithreaded application which uses Parallel Python (http://www.parallelpython.com) to analyze data in seperate processes, so it takes advantage of multiple CPUs and is truly concurrent. The results of the analysis are returned and I update my pytables file, which I think I have adequately protected with a mutex lock. After many iterations, I eventually get an error message that I am having trouble understanding: ----------------- Unhandled exception in thread started by Traceback (most recent call last): File "/usr/lib64/python2.5/site-packages/pp.py", line 494, in __run job.finalize(sresult) File "/usr/lib64/python2.5/site-packages/pp.py", line 53, in finalize self.__unpickle() File "/usr/lib64/python2.5/site-packages/pp.py", line 82, in __unpickle self.callback(*args) File "/home/darren/src/xpaxs/xpaxs-reorg/xpaxs/spectromicroscopy/advancedfitanalysis.py", line 249, in updateRecords File "/usr/lib/python2.5/site-packages/tables/group.py", line 854, in __getattr__ return self._f_getChild(name) File "/usr/lib/python2.5/site-packages/tables/group.py", line 736, in _f_getChild return self._v_file._getNode(childPath) File "/usr/lib/python2.5/site-packages/tables/file.py", line 918, in _getNode parentNode = self._reviveNode(parentPath) File "/usr/lib/python2.5/site-packages/tables/file.py", line 2219, in _reviveNode node = self._deadNodes.pop(nodePath) File "/usr/lib/python2.5/site-packages/tables/misc/lrucache.py", line 201, in pop self.__heap.remove(node) ValueError: list.remove(x): x not in list ------------- When I close my application, I get some additional output: ------------- Closing remaining open files: /home/darren/citrus_leaves.mca.h5... Error in atexit._run_exitfuncs: Traceback (most recent call last): File "/usr/lib64/python2.5/atexit.py", line 24, in _run_exitfuncs func(*targs, **kargs) File "/usr/lib/python2.5/site-packages/tables/file.py", line 2255, in close_open_files fileh.close() File "/usr/lib/python2.5/site-packages/tables/file.py", line 2064, in close lambda path: self._reviveNode(path)) File "/usr/lib/python2.5/site-packages/tables/file.py", line 2021, in _closeNodes node = getNode(nodePath) File "/usr/lib/python2.5/site-packages/tables/file.py", line 2064, in <lambda> lambda path: self._reviveNode(path)) File "/usr/lib/python2.5/site-packages/tables/file.py", line 2216, in _reviveNode "trying to revive non-dead node ``%s``" % nodePath AssertionError: trying to revive non-dead node ``/scan5/elementMaps/MassFraction/BrK`` Error in sys.exitfunc: Traceback (most recent call last): File "/usr/lib64/python2.5/atexit.py", line 24, in _run_exitfuncs func(*targs, **kargs) File "/usr/lib/python2.5/site-packages/tables/file.py", line 2255, in close_open_files fileh.close() File "/usr/lib/python2.5/site-packages/tables/file.py", line 2064, in close lambda path: self._reviveNode(path)) File "/usr/lib/python2.5/site-packages/tables/file.py", line 2021, in _closeNodes node = getNode(nodePath) File "/usr/lib/python2.5/site-packages/tables/file.py", line 2064, in <lambda> lambda path: self._reviveNode(path)) File "/usr/lib/python2.5/site-packages/tables/file.py", line 2216, in _reviveNode "trying to revive non-dead node ``%s``" % nodePath AssertionError: trying to revive non-dead node ``/scan5/elementMaps/MassFraction/BrK`` ------------- Does anyone have any thoughts? If I serialize the update of the pytables object, I am able to process the entire data set without any error messages. Does anyone have experience working with pytables in a multithreaded app that can describe any gotchas? Thank you, Darren ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Pytables-users mailing list Pytables-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pytables-users
